X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4H04 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.62930.2M potassium sodium tartate tetrahydrate, 0.1M sodium citrate, 2.0M ammonium sulfate, pH 5.6
Crystal Properties
Matthews coefficientSolvent content
2.7955.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.868α = 90
b = 131.271β = 90
c = 104.302γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702014-05-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.0Photon FactoryAR-NE3A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.650900.055182.5189858
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6395.20.2712.922.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT4H041.628.19180311954290.10.1830.1810.212RANDOM17.73
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.013
r_dihedral_angle_4_deg18.348
r_dihedral_angle_3_deg13.695
r_dihedral_angle_1_deg7.375
r_long_range_B_refined5.144
r_long_range_B_other5.117
r_scangle_other3.809
r_mcangle_it2.684
r_mcangle_other2.684
r_scbond_other2.583
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.013
r_dihedral_angle_4_deg18.348
r_dihedral_angle_3_deg13.695
r_dihedral_angle_1_deg7.375
r_long_range_B_refined5.144
r_long_range_B_other5.117
r_scangle_other3.809
r_mcangle_it2.684
r_mcangle_other2.684
r_scbond_other2.583
r_scbond_it2.582
r_angle_other_deg2.549
r_angle_refined_deg2.262
r_mcbond_it1.906
r_mcbond_other1.906
r_chiral_restr0.161
r_bond_refined_d0.025
r_gen_planes_other0.017
r_gen_planes_refined0.012
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9974
Nucleic Acid Atoms
Solvent Atoms947
Heterogen Atoms75

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing